Main data: [GEO (NCBI) - GSE271059]
{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE271059
Quantile Normalization and GEP score: [Ayers et al., 2017]
Loading data
Cleaning data
Replacing “Not_Available” with NA
Removing duplicates: distinct()
Standardizing names
Creating new metadata columns
Age_groups
TLS_status_bin
Normalizing gene expression
cpm_normalization
quantile_normalization
Computing GEP scores
Combining normalized counts with metadata
Preparing data for PCA/downstream analysis
Baseline tables
PCA on gene expression

TLS status does not strongly separate the samples
TLS group contains highly distinct outliers

Clear and distinct separation of samples by IDH status
Outlier subsets exist


